GenomeQuest™ Helps UC, Davis Researchers to Identify a New Virus from Declining Grapevines
News Nov 11, 2008
GenomeQuest, Inc. has announced researchers at the University of California, Davis used its recently announced On-Demand Informatics Solution to process and analyze next-generation sequencing data, successfully leading to identification of a new RNA virus from a declining Syrah grapevine cultivar.
The virus-hunting project was led by UC Davis researchers from Dr. Adib Rowhani’s lab, under the supervision of Dr. Maher Al Rwahnih. The researchers traced the composition and origin of a previously unknown virus that was suspected of causing a declining disease in California Syrah vineyards. This work supports efforts to help the wine industry with vineyard management and grape production.
The researchers used the Roche 454 platform to generate massive data files representing genetic material from samples of healthy and diseased plants. The GenomeQuest™ team, under the supervision of Dr. Jean-Jacques Codani, adapted a bioinformatics workflow to compute, from raw sequence data, a valuable database by grouping and classifying sequences that had high similarity to known organisms.
Sequences that did not have a match were grouped in such a manner that helped the researchers to find similarity between potential hidden viruses and known viruses.
UC Davis researchers were then able to access the database via the GenomeQuest web interface to select suspect sequences that did not have high similarities to known organisms, but had kinship with known viruses - ultimately identifying the elusive viral culprit by matching the sequences against those in the specialized viral database.
Dr. Adib Rowhani at UC Davis, said, “This successful identification of the suspected organism is truly groundbreaking research which will be of great practical benefit to the California wine industry – a fact that is a source of great pride to our UC Davis-based team.”